-
Notifications
You must be signed in to change notification settings - Fork 97
/
confidence_maps.py
554 lines (470 loc) · 22.9 KB
/
confidence_maps.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
"""Transformers for confidence map generation."""
import tensorflow as tf
import attr
from typing import List, Text, Union, Tuple
from sleap.nn.data.utils import make_grid_vectors
from sleap.nn.data.offset_regression import make_offsets, mask_offsets
def make_confmaps(
points: tf.Tensor, xv: tf.Tensor, yv: tf.Tensor, sigma: float
) -> tf.Tensor:
"""Make confidence maps from a set of points from a single instance.
Args:
points: A tensor of points of shape `(n_nodes, 2)` and dtype `tf.float32` where
the last axis corresponds to (x, y) pixel coordinates on the image. These
can contain NaNs to indicate missing points.
xv: Sampling grid vector for x-coordinates of shape `(grid_width,)` and dtype
`tf.float32`. This can be generated by
`sleap.nn.data.utils.make_grid_vectors`.
yv: Sampling grid vector for y-coordinates of shape `(grid_height,)` and dtype
`tf.float32`. This can be generated by
`sleap.nn.data.utils.make_grid_vectors`.
sigma: Standard deviation of the 2D Gaussian distribution sampled to generate
confidence maps.
Returns:
Confidence maps as a tensor of shape `(grid_height, grid_width, n_nodes)` of
dtype `tf.float32`.
Each channel of the confidence maps will contain the unnormalized PDF of a 2D
Gaussian distribution with a mean centered at the coordinates of the
corresponding point, and diagonal covariance matrix (i.e., the same standard
deviation for both dimensions).
When the point is perfectly aligned to the sampling grid, the value at that grid
coordinate is 1.0 since the PDF is not normalized.
If a point was missing (indicated by NaNs), the corresponding channel will
contain all zeros.
See also: sleap.nn.data.make_grid_vectors, make_multi_confmaps
"""
x = tf.reshape(tf.gather(points, [0], axis=1), [1, 1, -1])
y = tf.reshape(tf.gather(points, [1], axis=1), [1, 1, -1])
cm = tf.exp(
-((tf.reshape(xv, [1, -1, 1]) - x) ** 2 + (tf.reshape(yv, [-1, 1, 1]) - y) ** 2)
/ (2 * sigma ** 2)
)
cm = tf.math.maximum(0.0, cm) # Replaces NaNs with 0.
return cm
def make_multi_confmaps(
instances: tf.Tensor, xv: tf.Tensor, yv: tf.Tensor, sigma: float
) -> tf.Tensor:
"""Make confidence maps for multiple instances through reduction.
Args:
instances: A tensor of shape `(n_instances, n_nodes, 2)` and dtype `tf.float32`
containing instance points where the last axis corresponds to (x, y) pixel
coordinates on the image. This must be rank-3 even if a single instance is
present.
xv: Sampling grid vector for x-coordinates of shape `(grid_width,)` and dtype
`tf.float32`. This can be generated by
`sleap.nn.data.utils.make_grid_vectors`.
yv: Sampling grid vector for y-coordinates of shape `(grid_height,)` and dtype
`tf.float32`. This can be generated by
`sleap.nn.data.utils.make_grid_vectors`.
sigma: Standard deviation of the 2D Gaussian distribution sampled to generate
confidence maps.
Returns:
Confidence maps as a tensor of shape `(grid_height, grid_width, n_nodes)` of
dtype `tf.float32`.
Each channel will contain the elementwise maximum of the confidence maps
generated from all individual points for the associated node.
Notes:
The confidence maps are computed individually for each instance and immediately
max-reduced to avoid maintaining the entire set of all instance maps. This
enables memory-efficient generation of multi-instance maps for examples with
large numbers of instances.
See also: sleap.nn.data.make_grid_vectors, make_confmaps
"""
# Initialize output tensors.
grid_height = tf.shape(yv)[0]
grid_width = tf.shape(xv)[0]
n_nodes = tf.shape(instances)[1]
cms = tf.zeros((grid_height, grid_width, n_nodes), tf.float32)
# Eliminate instances completely outside of image.
in_img = (instances > 0) & (
instances < tf.reshape(tf.stack([xv[-1], yv[-1]], axis=0), [1, 1, 2])
)
in_img = tf.reduce_any(tf.reduce_all(in_img, axis=-1), axis=1)
in_img = tf.ensure_shape(in_img, [None])
instances = tf.boolean_mask(instances, in_img)
# Generate and reduce outputs by instance.
for points in instances:
cms_instance = make_confmaps(points, xv, yv, sigma=sigma)
cms = tf.maximum(cms, cms_instance)
return cms
def make_multi_confmaps_with_offsets(
instances: tf.Tensor,
xv: tf.Tensor,
yv: tf.Tensor,
stride: int,
sigma: float,
offsets_threshold: float,
) -> tf.Tensor:
"""Make confidence maps and offsets for multiple instances through reduction.
Args:
instances: A tensor of shape `(n_instances, n_nodes, 2)` and dtype `tf.float32`
containing instance points where the last axis corresponds to (x, y) pixel
coordinates on the image. This must be rank-3 even if a single instance is
present.
xv: Sampling grid vector for x-coordinates of shape `(grid_width,)` and dtype
`tf.float32`. This can be generated by
`sleap.nn.data.utils.make_grid_vectors`.
yv: Sampling grid vector for y-coordinates of shape `(grid_height,)` and dtype
`tf.float32`. This can be generated by
`sleap.nn.data.utils.make_grid_vectors`.
stride: Scaling factor for offset coordinates. The individual offset vectors
will be divided by this value. Useful for adjusting for strided sampling
grids so that the offsets point to the smaller grid coordinates.
sigma: Standard deviation of the 2D Gaussian distribution sampled to generate
confidence maps.
offsets_threshold: Minimum confidence map value below which offsets will be
replaced with zeros.
flatten_offsets: If `True`, the last two channels of the offset maps will be
flattened to produce rank-3 tensors. If `False`, the generated offset maps
will be rank-4 with shape `(height, width, n_nodes, 2)`.
Returns:
A tuple of `(confmaps, offsets)`.
`confmaps` are confidence maps as a tensor of shape
`(grid_height, grid_width, n_nodes)` and dtype `tf.float32`.
Each channel will contain the elementwise maximum of the confidence maps
generated from all individual points for the associated node.
`offsets` are offset maps as a `tf.Tensor` of shape
`(grid_height, grid_width, n_nodes, 2)` and dtype `tf.float32`. The last axis
corresponds to the x- and y-offsets at each grid point for each node.
Notes:
The confidence maps and offsets are computed individually for each instance
and immediately max-reduced to avoid maintaining the entire set of all instance
maps. This enables memory-efficient generation of multi-instance maps for
examples with large numbers of instances.
See also: sleap.nn.data.make_grid_vectors, make_confmaps, make_multi_confmaps
"""
# Initialize output tensors.
grid_height = tf.shape(yv)[0]
grid_width = tf.shape(xv)[0]
n_nodes = tf.shape(instances)[1]
cms = tf.zeros((grid_height, grid_width, n_nodes), tf.float32)
offsets = tf.zeros((grid_height, grid_width, n_nodes, 2), tf.float32)
# Eliminate instances completely outside of image.
in_img = (instances > 0) & (
instances < tf.reshape(tf.stack([xv[-1], yv[-1]], axis=0), [1, 1, 2])
)
in_img = tf.reduce_any(tf.reduce_all(in_img, axis=-1), axis=1)
in_img = tf.ensure_shape(in_img, [None])
instances = tf.boolean_mask(instances, in_img)
# Generate and reduce outputs by instance.
for points in instances:
cms_instance = make_confmaps(points, xv, yv, sigma=sigma)
cms = tf.maximum(cms, cms_instance)
offsets_instance = mask_offsets(
make_offsets(points, xv, yv, stride=stride),
cms_instance,
threshold=offsets_threshold,
)
offsets += offsets_instance
return cms, offsets
@attr.s(auto_attribs=True)
class MultiConfidenceMapGenerator:
"""Transformer to generate multi-instance confidence maps.
Attributes:
sigma: Standard deviation of the 2D Gaussian distribution sampled to generate
confidence maps. This defines the spread in units of the input image's grid,
i.e., it does not take scaling in previous steps into account.
output_stride: Relative stride of the generated confidence maps. This is
effectively the reciprocal of the output scale, i.e., increase this to
generate confidence maps that are smaller than the input images.
centroids: If `True`, generate confidence maps for centroids rather than
instance points.
with_offsets: If `True`, also return offsets for refining the peaks.
offsets_threshold: Minimum confidence map value below which offsets will be
replaced with zeros.
flatten_offsets: If `True`, the last two channels of the offset maps will be
flattened to produce rank-3 tensors. If `False`, the generated offset maps
will be rank-4 with shape `(height, width, n_nodes, 2)`.
"""
sigma: float = 1.0
output_stride: int = 1
centroids: bool = False
with_offsets: bool = False
offsets_threshold: float = 0.2
flatten_offsets: bool = True
@property
def input_keys(self) -> List[Text]:
"""Return the keys that incoming elements are expected to have."""
if self.centroids:
return ["image", "centroids"]
else:
return ["image", "instances"]
@property
def output_keys(self) -> List[Text]:
"""Return the keys that outgoing elements will have."""
if self.centroids:
keys = self.input_keys + ["centroid_confidence_maps"]
else:
keys = self.input_keys + ["confidence_maps"]
if self.with_offsets:
keys.append("offsets")
return keys
def transform_dataset(self, input_ds: tf.data.Dataset) -> tf.data.Dataset:
"""Create a dataset that contains the generated confidence maps.
Args:
input_ds: A dataset with elements that contain the keys `"image"`, `"scale"`
and either "instances" or "centroids" depending on whether the
`centroids` attribute is set to `True`.
Returns:
A `tf.data.Dataset` with the same keys as the input, as well as a
`"confidence_maps"` or `"centroid_confidence_maps"` key containing the
generated confidence maps.
If the `with_offsets` attribute is `True`, example will contain a
`"offsets"` key.
Notes:
The output stride is relative to the current scale of the image. To map
points on the confidence maps to the raw image, first multiply them by the
output stride, and then scale the x- and y-coordinates by the `"scale"` key.
Importantly, the `sigma` will be proportional to the current image grid, not
the original grid prior to scaling operations.
"""
# Infer image dimensions to generate the full scale sampling grid.
test_example = next(iter(input_ds))
image_height = test_example["image"].shape[0]
image_width = test_example["image"].shape[1]
# Generate sampling grid vectors.
xv, yv = make_grid_vectors(
image_height=image_height,
image_width=image_width,
output_stride=self.output_stride,
)
def generate_multi_confmaps(example):
"""Local processing function for dataset mapping."""
if self.centroids:
points = tf.expand_dims(example["centroids"], axis=1)
cm_key = "centroid_confidence_maps"
else:
points = example["instances"]
cm_key = "confidence_maps"
if self.with_offsets:
cms, offsets = make_multi_confmaps_with_offsets(
points,
xv,
yv,
self.output_stride,
self.sigma * self.output_stride,
self.offsets_threshold,
)
example["offsets"] = offsets
if self.flatten_offsets:
shape = tf.shape(example["offsets"])
example["offsets"] = tf.reshape(
example["offsets"], [shape[0], shape[1], -1]
)
else:
cms = make_multi_confmaps(
points, xv, yv, self.sigma * self.output_stride
)
example[cm_key] = cms
return example
# Map transformation.
output_ds = input_ds.map(
generate_multi_confmaps, num_parallel_calls=tf.data.experimental.AUTOTUNE
)
return output_ds
@attr.s(auto_attribs=True)
class InstanceConfidenceMapGenerator:
"""Transformer to generate instance-centered confidence maps.
Attributes:
sigma: Standard deviation of the 2D Gaussian distribution sampled to generate
confidence maps. This defines the spread in units of the input image's grid,
i.e., it does not take scaling in previous steps into account.
output_stride: Relative stride of the generated confidence maps. This is
effectively the reciprocal of the output scale, i.e., increase this to
generate confidence maps that are smaller than the input images.
all_instances: If `True`, will also generate the multi-instance confidence maps.
with_offsets: If `True`, also return offsets for refining the peaks.
offsets_threshold: Minimum confidence map value below which offsets will be
replaced with zeros.
flatten_offsets: If `True`, the last two channels of the offset maps will be
flattened to produce rank-3 tensors. If `False`, the generated offset maps
will be rank-4 with shape `(height, width, n_nodes, 2)`.
"""
sigma: float = 1.0
output_stride: int = 1
all_instances: bool = False
with_offsets: bool = False
offsets_threshold: float = 0.2
flatten_offsets: bool = True
@property
def input_keys(self) -> List[Text]:
"""Return the keys that incoming elements are expected to have."""
if self.all_instances:
return ["instance_image", "center_instance", "all_instances"]
else:
return ["instance_image", "center_instance"]
@property
def output_keys(self) -> List[Text]:
"""Return the keys that outgoing elements will have."""
keys = self.input_keys + ["instance_confidence_maps"]
if self.with_offsets:
keys.append("offsets")
if self.all_instances:
keys.append("all_instance_confidence_maps")
if self.with_offsets:
keys.append("all_instance_offsets")
return keys
def transform_dataset(self, input_ds: tf.data.Dataset) -> tf.data.Dataset:
"""Create a dataset that contains the generated confidence maps.
Args:
input_ds: A dataset with elements that contain the keys `"instance_image"`,
`"center_instance"` and, if the attribute `all_instances` is `True`,
`"all_instances"`.
Returns:
A `tf.data.Dataset` with the same keys as the input, as well as
`"instance_confidence_maps"` and, if the attribute `all_instances` is
`True`, `"all_instance_confidence_maps"` keys containing the generated
confidence maps.
If the `with_offsets` attribute is `True`, example will contain a
`"offsets"` key.
Notes:
The output stride is relative to the current scale of the image. To map
points on the confidence maps to the raw image, first multiply them by the
output stride, and then scale the x- and y-coordinates by the `"scale"` key.
Importantly, the `sigma` will be proportional to the current image grid, not
the original grid prior to scaling operations.
"""
# Infer image dimensions to generate sampling grid.
test_example = next(iter(input_ds))
image_height = test_example["instance_image"].shape[0]
image_width = test_example["instance_image"].shape[1]
# Generate sampling grid vectors.
xv, yv = make_grid_vectors(
image_height=image_height,
image_width=image_width,
output_stride=self.output_stride,
)
def generate_confmaps(example):
"""Local processing function for dataset mapping."""
example["instance_confidence_maps"] = make_confmaps(
example["center_instance"],
xv=xv,
yv=yv,
sigma=self.sigma * self.output_stride,
)
if self.with_offsets:
example["offsets"] = mask_offsets(
make_offsets(
example["center_instance"], xv, yv, stride=self.output_stride
),
example["instance_confidence_maps"],
self.offsets_threshold,
)
if self.flatten_offsets:
shape = tf.shape(example["offsets"])
example["offsets"] = tf.reshape(
example["offsets"], [shape[0], shape[1], -1]
)
if self.all_instances:
if self.with_offsets:
cms, offsets = make_multi_confmaps_with_offsets(
example["all_instances"],
xv,
yv,
self.output_stride,
self.sigma * self.output_stride,
offsets_threshold=self.offsets_threshold,
)
example["all_instance_offsets"] = offsets
if self.flatten_offsets:
shape = tf.shape(example["all_instance_offsets"])
example["all_instance_offsets"] = tf.reshape(
example["all_instance_offsets"], [shape[0], shape[1], -1]
)
else:
cms = make_multi_confmaps(
example["all_instances"],
xv=xv,
yv=yv,
sigma=self.sigma * self.output_stride,
)
example["all_instance_confidence_maps"] = cms
return example
# Map transformation.
output_ds = input_ds.map(
generate_confmaps, num_parallel_calls=tf.data.experimental.AUTOTUNE
)
return output_ds
@attr.s(auto_attribs=True)
class SingleInstanceConfidenceMapGenerator:
"""Transformer to generate single-instance confidence maps.
Attributes:
sigma: Standard deviation of the 2D Gaussian distribution sampled to generate
confidence maps. This defines the spread in units of the input image's grid,
i.e., it does not take scaling in previous steps into account.
output_stride: Relative stride of the generated confidence maps. This is
effectively the reciprocal of the output scale, i.e., increase this to
generate confidence maps that are smaller than the input images.
with_offsets: If `True`, also return offsets for refining the peaks.
offsets_threshold: Minimum confidence map value below which offsets will be
replaced with zeros.
flatten_offsets: If `True`, the last two channels of the offset maps will be
flattened to produce rank-3 tensors. If `False`, the generated offset maps
will be rank-4 with shape `(height, width, n_nodes, 2)`.
"""
sigma: float = 1.0
output_stride: int = 1
with_offsets: bool = False
offsets_threshold: float = 0.2
flatten_offsets: bool = True
@property
def input_keys(self) -> List[Text]:
"""Return the keys that incoming elements are expected to have."""
return ["image", "instances"]
@property
def output_keys(self) -> List[Text]:
"""Return the keys that outgoing elements will have."""
keys = self.input_keys + ["points", "confidence_maps"]
if self.with_offsets:
keys.append("offsets")
return keys
def transform_dataset(self, input_ds: tf.data.Dataset) -> tf.data.Dataset:
"""Create a dataset that contains the generated confidence maps.
Args:
input_ds: A dataset with elements that contain the keys `"instances"` and
`"image"`.
Returns:
A `tf.data.Dataset` with the same keys as the input, as well as
`"confidence_maps"` containing the generated confidence maps.
Notes:
The output stride is relative to the current scale of the image. To map
points on the confidence maps to the raw image, first multiply them by the
output stride, and then scale the x- and y-coordinates by the "scale" key.
Importantly, the `sigma` will be proportional to the current image grid, not
the original grid prior to scaling operations.
"""
# Infer image dimensions to generate sampling grid.
test_example = next(iter(input_ds))
image_height = test_example["image"].shape[0]
image_width = test_example["image"].shape[1]
# Generate sampling grid vectors.
xv, yv = make_grid_vectors(
image_height=image_height,
image_width=image_width,
output_stride=self.output_stride,
)
def generate_confmaps(example):
"""Local processing function for dataset mapping."""
# Pull out first instance as (n_nodes, 2) tensor.
example["points"] = tf.gather(example["instances"], 0, axis=0)
# Generate confidence maps.
example["confidence_maps"] = make_confmaps(
example["points"], xv=xv, yv=yv, sigma=self.sigma * self.output_stride
)
if self.with_offsets:
example["offsets"] = mask_offsets(
make_offsets(example["points"], xv, yv, stride=self.output_stride),
example["confidence_maps"],
self.offsets_threshold,
)
if self.flatten_offsets:
shape = tf.shape(example["offsets"])
example["offsets"] = tf.reshape(
example["offsets"], [shape[0], shape[1], -1]
)
return example
# Map transformation.
output_ds = input_ds.map(
generate_confmaps, num_parallel_calls=tf.data.experimental.AUTOTUNE
)
return output_ds